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dc.contributor.authorAhmadi, Asal
dc.contributor.authorKhezri, Abdolrahman
dc.contributor.authorNørstebø, Håvard
dc.contributor.authorAhmad, Rafi
dc.date.accessioned2024-02-01T14:55:44Z
dc.date.available2024-02-01T14:55:44Z
dc.date.created2023-01-06T20:25:36Z
dc.date.issued2023
dc.identifier.issn1664-302X
dc.identifier.urihttps://hdl.handle.net/11250/3115127
dc.description.abstractIntroduction: Rapid and accurate diagnosis of causative pathogens in mastitis would minimize the imprudent use of antibiotics and, therefore, reduce the spread of antimicrobial resistance. Whole genome sequencing offers a unique opportunity to study the microbial community and antimicrobial resistance (AMR) in mastitis. However, the complexity of milk samples and the presence of a high amount of host DNA in milk from infected udders often make this very challenging. Methods: Here, we tested 24 bovine milk samples (18 mastitis and six non-mastitis) using four different commercial kits (Qiagens’ DNeasy® PowerFood® Microbial, Norgens’ Milk Bacterial DNA Isolation, and Molzyms’ MolYsis™ Plus and Complete5) in combination with filtration, low-speed centrifugation, nuclease, and 10% bile extract of male bovine (Ox bile). Isolated DNA was quantified, checked for the presence/absence of host and pathogen using PCR and sequenced using MinION nanopore sequencing. Bioinformatics analysis was performed for taxonomic classification and antimicrobial resistance gene detection. Results: The results showed that kits designed explicitly for bacterial DNA isolation from food and dairy matrices could not deplete/minimize host DNA. Following using MolYsis™ Complete 5 + 10% Ox bile + micrococcal nuclease combination, on average, 17% and 66.5% of reads were classified as bovine and Staphylococcus aureus reads, respectively. This combination also effectively enriched other mastitis pathogens, including Escherichia coli and Streptococcus dysgalactiae. Furthermore, using this approach, we identified important AMR genes such as Tet (A), Tet (38), fosB-Saur, and blaZ. We showed that even 40 min of the MinION run was enough for bacterial identification and detecting the first AMR gene. Conclusion: We implemented an effective method (sensitivity of 100% and specificity of 92.3%) for host DNA removal and bacterial DNA enrichment (both gram-negative and positive) directly from bovine mastitis milk. To the best of our knowledge, this is the first culture- and amplification-independent study using nanopore-based metagenomic sequencing for real-time detection of the pathogen (within 5 hours) and the AMR profile (within 5–9 hours), in mastitis milk samples. These results provide a promising and potential future on-farm adaptable approach for better clinical management of mastitis.en_US
dc.language.isoengen_US
dc.rightsNavngivelse 4.0 Internasjonal*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/deed.no*
dc.subjectmastitisen_US
dc.subjectstaphylococcus aureusen_US
dc.subjectudder infectionsen_US
dc.subjectnanopore sequencing technologyen_US
dc.subjectculture-independent sequencingen_US
dc.subjectrapid diagnosisen_US
dc.subjectantibiotic resistanceen_US
dc.subjectmilken_US
dc.titleA culture-, amplification-independent, and rapid method for identification of pathogens and antibiotic resistance profile in bovine mastitis milken_US
dc.title.alternativeA culture-, amplification-independent, and rapid method for identification of pathogens and antibiotic resistance profile in bovine mastitis milken_US
dc.typePeer revieweden_US
dc.typeJournal articleen_US
dc.description.versionpublishedVersionen_US
dc.rights.holder© 2023 Ahmadi, Khezri, Nørstebø and Ahmad.en_US
dc.subject.nsiVDP::Matematikk og Naturvitenskap: 400en_US
dc.source.volume13en_US
dc.source.journalFrontiers in Microbiologyen_US
dc.identifier.doi10.3389/fmicb.2022.1104701
dc.identifier.cristin2102367
cristin.ispublishedtrue
cristin.fulltextoriginal
cristin.qualitycode2


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Navngivelse 4.0 Internasjonal
Except where otherwise noted, this item's license is described as Navngivelse 4.0 Internasjonal